SpliceTrap on Biowulf
SpliceTrap is a statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing. SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is included, skipped or subjected to size variations due to alternative 3?/5? splice sites or Intron Retention. In addition, SpliceTrap can quantify alternative splicing within a single cellular condition, with no need of a background set of reads.
SpliceTrap was developed by Wu et al at Cold Spring Harbor Laboratory. [SpliceTrap website] [SpliceTrap publication]
The databases hg18, hg19, mm9, rn4 are available for SpliceTrap.
Running a SpliceTrap job on Biowulf
The splicetrap module on Biowulf also loads R and bowtie.
Do not use SpliceTrap's qsub command. This is designed for Sun Grid Engine, and the Biowulf cluster uses a different batch system.
The following example uses the downloadable test files from http://rulai.cshl.edu/splicetrap/. Set up a batch script along the following lines:
#PBS -N SpliceTrap
module load splicetrap
SpliceTrap -m bowtie -d hg18 -1 HeLa_1.r1.fa -2 HeLa_1.r2.fa -o myfile.out -p 24 -force-no-qsub
Since 24 threads (-p 24) are requested for the Bowtie run, the job must be submitted to a node with at least 24 cores.
qsub -l nodes=1:c24:g24 splicetrap.bat